def test_both_types(self):
"""Test each object store configures files correctly.
"""
i = 0
with self.dataset_populator.test_history() as history_id:
# Loop breaks once each object store has at least once file of each type.
while True:
hda = self.dataset_populator.new_dataset(history_id, content=TEST_INPUT_FILES_CONTENT, wait=True)
content = self.dataset_populator.get_history_dataset_content(history_id, hda["id"])
assert content.strip() == TEST_INPUT_FILES_CONTENT
files1_count = files_count(self.files1_path)
files2_count = files_count(self.files2_path)
if files1_count and files2_count:
break
i += 1
if i > 50:
raise Exception("Problem with logic of test, randomly each object store should have at least one file by now")
def strip_to_id(x):
match = re.match(r'dataset_(.*)\.dat', os.path.basename(x))
assert match
return match.group(1)
files1_paths = [strip_to_id(p) for p in _get_datasets_files_in_path(self.files1_path)]
files2_paths = [strip_to_id(p) for p in _get_datasets_files_in_path(self.files2_path)]
for files1_path in files1_paths:
assert is_uuid(files1_path)
for files2_path in files2_paths:
assert files2_path.isdigit()
def directory_hash_id( id ):
"""
>>> directory_hash_id( 100 )
['000']
>>> directory_hash_id( "90000" )
['090']
>>> directory_hash_id("777777777")
['000', '777', '777']
>>> directory_hash_id("135ee48a-4f51-470c-ae2f-ce8bd78799e6")
['1', '3', '5']
"""
s = str( id )
l = len( s )
# Shortcut -- ids 0-999 go under ../000/
if l < 4:
return [ "000" ]
if not is_uuid(s):
# Pad with zeros until a multiple of three
padded = ( ( 3 - len( s ) % 3 ) * "0" ) + s
# Drop the last three digits -- 1000 files per directory
padded = padded[:-3]
# Break into chunks of three
return [ padded[ i * 3 : (i + 1 ) * 3 ] for i in range( len( padded ) // 3 ) ]
else:
# assume it is a UUID
return list(iter(s[0:3]))
def directory_hash_id(id):
"""
>>> directory_hash_id( 100 )
['000']
>>> directory_hash_id( "90000" )
['090']
>>> directory_hash_id("777777777")
['000', '777', '777']
>>> directory_hash_id("135ee48a-4f51-470c-ae2f-ce8bd78799e6")
['1', '3', '5']
"""
s = str(id)
l = len(s)
# Shortcut -- ids 0-999 go under ../000/
if l < 4:
return ["000"]
if not is_uuid(s):
# Pad with zeros until a multiple of three
padded = ((3 - len(s) % 3) * "0") + s
# Drop the last three digits -- 1000 files per directory
padded = padded[:-3]
# Break into chunks of three
return [padded[i * 3:(i + 1) * 3] for i in range(len(padded) // 3)]
else:
# assume it is a UUID
return list(iter(s[0:3]))
def _get_dynamic_tool(self, trans, request_id):
manager = self.app.dynamic_tools_manager
if util.is_uuid(request_id):
dynamic_tool = manager.get_tool_by_uuid(request_id)
else:
dynamic_tool = manager.get_tool_by_id(
trans.security.decode_id(request_id))
if dynamic_tool is None:
raise ObjectNotFound()
return dynamic_tool
def __get_stored_workflow( self, trans, workflow_id ):
if util.is_uuid(workflow_id):
# see if they have passed in the UUID for a workflow that is attached to a stored workflow
workflow_uuid = uuid.UUID(workflow_id)
stored_workflow = trans.sa_session.query(trans.app.model.StoredWorkflow).filter( and_(
trans.app.model.StoredWorkflow.latest_workflow_id == trans.app.model.Workflow.id,
trans.app.model.Workflow.uuid == workflow_uuid
)).first()
if stored_workflow is None:
raise exceptions.ObjectNotFound( "Workflow not found: %s" % workflow_id )
else:
workflow_id = self.decode_id( workflow_id )
query = trans.sa_session.query( trans.app.model.StoredWorkflow )
stored_workflow = query.get( workflow_id )
if stored_workflow is None:
raise exceptions.ObjectNotFound( "No such workflow found." )
return stored_workflow
def __get_stored_workflow( self, trans, workflow_id ):
if util.is_uuid(workflow_id):
# see if they have passed in the UUID for a workflow that is attached to a stored workflow
workflow_uuid = uuid.UUID(workflow_id)
stored_workflow = trans.sa_session.query(trans.app.model.StoredWorkflow).filter( and_(
trans.app.model.StoredWorkflow.latest_workflow_id == trans.app.model.Workflow.id,
trans.app.model.Workflow.uuid == workflow_uuid
)).first()
if stored_workflow is None:
raise exceptions.ObjectNotFound( "Workflow not found: %s" % workflow_id )
else:
workflow_id = self.decode_id( workflow_id )
query = trans.sa_session.query( trans.app.model.StoredWorkflow )
stored_workflow = query.get( workflow_id )
if stored_workflow is None:
raise exceptions.ObjectNotFound( "No such workflow found." )
return stored_workflow
def get_stored_workflow(self, trans, workflow_id):
""" Use a supplied ID (UUID or encoded stored workflow ID) to find
a workflow.
"""
if util.is_uuid(workflow_id):
# see if they have passed in the UUID for a workflow that is attached to a stored workflow
workflow_uuid = uuid.UUID(workflow_id)
workflow_query = trans.sa_session.query(trans.app.model.StoredWorkflow).filter(and_(
trans.app.model.StoredWorkflow.latest_workflow_id == trans.app.model.Workflow.id,
trans.app.model.Workflow.uuid == workflow_uuid
))
else:
workflow_id = decode_id(self.app, workflow_id)
workflow_query = trans.sa_session.query(trans.app.model.StoredWorkflow).\
filter(trans.app.model.StoredWorkflow.id == workflow_id)
stored_workflow = workflow_query.options(joinedload('annotations'),
joinedload('tags'),
subqueryload('latest_workflow').joinedload('steps').joinedload('*')).first()
if stored_workflow is None:
raise exceptions.ObjectNotFound("No such workflow found.")
return stored_workflow
